UBP40_MOUSE
ID UBP40_MOUSE Reviewed; 1235 AA.
AC Q8BWR4; Q08EB7; Q148V0; Q3TLV1; Q3TMN0; Q3V1R4; Q5EBN6;
DT 10-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT 09-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 40;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 40;
DE AltName: Full=Ubiquitin thioesterase 40;
DE AltName: Full=Ubiquitin-specific-processing protease 40;
GN Name=Usp40;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 4), AND NUCLEOTIDE
RP SEQUENCE [LARGE SCALE MRNA] OF 1-1140 AND 967-1235 (ISOFORM 1).
RC STRAIN=C57BL/6J; TISSUE=Embryo, Liver, Lung, and Mammary gland;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
RC STRAIN=C57BL/6J; TISSUE=Eye;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=17242355; DOI=10.1073/pnas.0609836104;
RA Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.;
RT "Large-scale phosphorylation analysis of mouse liver.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brown adipose tissue, Pancreas, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide
CC and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-
CC residue protein attached to proteins as an intracellular targeting
CC signal).; EC=3.4.19.12;
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=4;
CC Name=1;
CC IsoId=Q8BWR4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8BWR4-2; Sequence=VSP_022174;
CC Name=3;
CC IsoId=Q8BWR4-3; Sequence=VSP_022171;
CC Name=4;
CC IsoId=Q8BWR4-4; Sequence=VSP_022172, VSP_022173;
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR EMBL; AK050239; BAC34140.1; -; mRNA.
DR EMBL; AK132295; BAE21086.1; -; mRNA.
DR EMBL; AK165849; BAE38411.1; -; mRNA.
DR EMBL; AK166303; BAE38691.1; -; mRNA.
DR EMBL; BC089376; AAH89376.1; -; mRNA.
DR EMBL; BC117957; AAI17958.1; -; mRNA.
DR EMBL; BC117958; AAI17959.1; -; mRNA.
DR CCDS; CCDS15137.1; -. [Q8BWR4-2]
DR CCDS; CCDS78645.1; -. [Q8BWR4-1]
DR RefSeq; NP_001028463.1; NM_001033291.2. [Q8BWR4-2]
DR RefSeq; NP_001185502.1; NM_001198573.1. [Q8BWR4-1]
DR AlphaFoldDB; Q8BWR4; -.
DR BioGRID; 230617; 2.
DR STRING; 10090.ENSMUSP00000038533; -.
DR MEROPS; C19.069; -.
DR iPTMnet; Q8BWR4; -.
DR PhosphoSitePlus; Q8BWR4; -.
DR EPD; Q8BWR4; -.
DR MaxQB; Q8BWR4; -.
DR PaxDb; Q8BWR4; -.
DR PeptideAtlas; Q8BWR4; -.
DR PRIDE; Q8BWR4; -.
DR ProteomicsDB; 297700; -. [Q8BWR4-1]
DR ProteomicsDB; 297701; -. [Q8BWR4-2]
DR ProteomicsDB; 297702; -. [Q8BWR4-3]
DR ProteomicsDB; 297703; -. [Q8BWR4-4]
DR Antibodypedia; 965; 124 antibodies from 23 providers.
DR DNASU; 227334; -.
DR Ensembl; ENSMUST00000040783; ENSMUSP00000038533; ENSMUSG00000005501. [Q8BWR4-2]
DR Ensembl; ENSMUST00000187758; ENSMUSP00000140107; ENSMUSG00000005501. [Q8BWR4-1]
DR GeneID; 227334; -.
DR KEGG; mmu:227334; -.
DR UCSC; uc007bxw.1; mouse. [Q8BWR4-2]
DR UCSC; uc007bxx.1; mouse. [Q8BWR4-1]
DR UCSC; uc007bxz.1; mouse. [Q8BWR4-4]
DR CTD; 55230; -.
DR MGI; MGI:2443184; Usp40.
DR VEuPathDB; HostDB:ENSMUSG00000005501; -.
DR eggNOG; KOG1863; Eukaryota.
DR GeneTree; ENSGT00940000157267; -.
DR HOGENOM; CLU_009719_0_0_1; -.
DR InParanoid; Q8BWR4; -.
DR OMA; NHPQIFQ; -.
DR OrthoDB; 77113at2759; -.
DR PhylomeDB; Q8BWR4; -.
DR TreeFam; TF106281; -.
DR BioGRID-ORCS; 227334; 1 hit in 73 CRISPR screens.
DR ChiTaRS; Usp40; mouse.
DR PRO; PR:Q8BWR4; -.
DR Proteomes; UP000000589; Chromosome 1.
DR RNAct; Q8BWR4; protein.
DR Bgee; ENSMUSG00000005501; Expressed in humerus cartilage element and 208 other tissues.
DR ExpressionAtlas; Q8BWR4; baseline and differential.
DR Genevisible; Q8BWR4; MM.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IBA:GO_Central.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IBA:GO_Central.
DR GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR GO; GO:0031647; P:regulation of protein stability; IBA:GO_Central.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR033384; USP40.
DR InterPro; IPR018200; USP_CS.
DR InterPro; IPR028889; USP_dom.
DR PANTHER; PTHR24006:SF644; PTHR24006:SF644; 1.
DR Pfam; PF00443; UCH; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS00972; USP_1; 1.
DR PROSITE; PS00973; USP_2; 1.
DR PROSITE; PS50235; USP_3; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Hydrolase; Protease; Reference proteome;
KW Thiol protease; Ubl conjugation pathway.
FT CHAIN 1..1235
FT /note="Ubiquitin carboxyl-terminal hydrolase 40"
FT /id="PRO_0000080671"
FT DOMAIN 41..482
FT /note="USP"
FT ACT_SITE 50
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT ACT_SITE 305
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT VAR_SEQ 1..128
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_022171"
FT VAR_SEQ 490..501
FT /note="ARANPRYRVPCH -> GMENKKCSALLC (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_022172"
FT VAR_SEQ 502..1235
FT /note="Missing (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_022173"
FT VAR_SEQ 795..883
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_022174"
FT CONFLICT 201
FT /note="E -> A (in Ref. 1; BAE38691)"
FT /evidence="ECO:0000305"
FT CONFLICT 943
FT /note="A -> E (in Ref. 2; AAH89376)"
FT /evidence="ECO:0000305"
FT CONFLICT 1134
FT /note="S -> N (in Ref. 1; BAE38411)"
FT /evidence="ECO:0000305"
FT CONFLICT 1142
FT /note="R -> K (in Ref. 2; AAH89376)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1235 AA; 139952 MW; CBAC7A6A0CACE03C CRC64;
MFGNLFEEDY SSVSSSQYGR GKKLKTKGLE PPAPREFTNL SGIRNQGGTC YLSSLLQTLH
FTPEFREALF SLGPEELGSL EDKDKPDAKV RIIPLQLQRL FAQLLLLDQE AASTIDLTDS
FGWTNDEEMR QHDVQELNRI LFSALETSLV GTSGHDLIHR LYHGTIVNQI VCKECKNISE
RQEDFLDLTV AVKNVSGLED ELCNMYVEEE IFDYDNLYHC GTCDRLVKAA KSAKLRKLPP
FLTISLLRFN FDFVKCERYK DTSCYTFPLR INLKPFCEQS ELDDMEYMYD LFSVIIHKGG
CYGGHYHVYI KDVDHLGNWQ CQEEISDTNV NVKAPQSEEE ANDPLVVLKT ILLQEEANQI
PVDQLGQKLL KKTGISWNKK YRKQHGPLRK FLQLHPQIFL LSTDESTVSL LRNHLTQAPS
DLQSCEQILH TLASESPGLN DDTSCPHWFD INDSKVHPIR EKDITQQFQG KESAYMLFYR
KATLQRPPEA RANPRYRVPC HLLKEMDAAN ILLQMRRAEC DSANSTFELH LHLGPHYRFF
NGALHPAVSE TESVWDLTFD KRKTLGDLRQ SIFQLLECWE GDMVLSVAKR VPAGLHVYHT
LDGDDLTLCE AEVADGEDIF VWNGVEVGGV QIQTGFDCEP LLLNILHLEL SGEGSKCEQL
VESPHVFPAN AEVGAVFTAL GTPAGAILMN SVESADGECW TAVPKEDMKK TFREQGLRNG
SLILVQDSDS DNNSLLPKQG RWTNSMNELN WLQVKNFCQS ESEEKQVQIA VTMHTVVFDI
RIKAIKELKL MKELAENSCL RPIDRNGKLL CPVPDSSTLE EAEVKMGSSV GLCLGKAPTS
SQLFLFFALG TDIHPGAEMD IIVEETLSVR DCLKIMLEKS GQQGEIWHLR KMDWCYEAGE
PLCEEDATLK ELMIRSGDTL LLTEGKLPPP GHLKMPIWWY QPARLSGHCE SRDHLNCAFS
QDSTWRAAPT QGAPGPEPAE VSLLYLGDME ISEEATLVEL KSQALALPSV SKLAVQSTAL
LRVWTVESKR PSRLLRTNWR QLKEYRLGRR AELCLELLQK EEDLGPRDVL LRTQLRIPGE
RAYSLATDLI WDTTRGWTAG SLRQRVADFY SLPVEKIEIA KYFPEKFEWL PISSWNQQVA
KRKKKKNQDT LQGGPYYLKD GDTIGIKNLL FDDNDDFSTI RDDIGKENQK RLALEKKKSR
EVHRAQSSDL FSNAGVPARF RGPEASLSIH VASFR
